The aeolid nudibranch Caloria elegans (Facelinidae) is quite common in the Mediterranean Sea and eastern Atlantic Ocean and is easily recognized by the presence of a typical black spot at the apical portion of its cerata. Facelina quatrefagesi (Facelinidae) was long considered as a synonym of C. elegans until recently, when it was re-evaluated as a valid species based mainly on rhinophore morphology. In order to definitively assess the status of these aeolid taxa, we employed an integrative taxonomy approach using the nuclear H3 and the two mitochondrial cytochrome oxidase subunit I and 16S markers. The molecular analyses clearly showed that, although morphologically closely related to C. elegans, F. quatrefagesi is a valid species.